Bibplography

Bibliography Setup

The bibliography is loaded and the DOIs, ISBNs and ISSNs are extracted.

Introduction

This report assesses the following in regards to the provided bibliography named bibliography:

Remarks: - Group ID is in the json, but not in the csv. The group ID makes it possible to directly jump to the reference in the Zotero Library online.

Data Quality of the Bibliography

Cleanliness of bibliography

One measure of the cleanliness of a Bibliography is assessed by checking the number of references that have a DOI. The following table gives an overview over some numbers regarding the DOIs, ISBNs and ISSNs in the bibliography.

Entries with DOIs, ISBNs or ISSNs

To identify a reference, the most widely used identifier is the DOI. The following table shows the number of references with a DOI and the number of unique DOIs.

To consider duplicate ISBNs or ISSNs as duplicates entries in the library is not waranted as e.g. differenc chapters of a book can be separate entries in the library and therefore lead toi duplicates.

DOIs: 746 (67.8181818%) - 4 duplicates
ISBNss: 92 (8.3636364%) - 2 duplicates
ISBNss: 692 (62.9090909%) - 443 duplicates

The following DOIs are duplicates in the bibliography. This table should be empty.

Show the code

#|
if (sum(duplicated(bibliography$dois)) > 0) {
    data <- data.frame(
        Type = "doi",
        Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', bibliography$dois[duplicated(bibliography$dois)], bibliography$dois[duplicated(bibliography$dois)])
    )
} else {
    data <- data.frame(
        Type = "doi",
        Identifier = NA
    )
}

data |>
    knitr::kable(
        caption = "Duplicate DOIs in the Bibliography",
        escape = FALSE
    )

Duplicate DOIs in the Bibliography
Type	Identifier
doi	10.1016/j.gloenvcha.2008.02.001
doi	10.1016/j.gloenvcha.2012.06.001
doi	10.1016/j.gloenvcha.2012.06.001
doi	10.1016/j.pocean.2010.09.001

Show the code

rm(data)

DOIs in Open Alex

To validate the existence and validity of the DOIs, we check if the DOIs are in the OpenAlex database.

Of the 742 unique DOIs in the library, 88 (11.8598383%) are in not in OpenAlex.

Show the code

data.frame(
    Type = "doi",
    Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', metrics$dois_not_in_oa, metrics$dois_not_in_oa)
) |>
    IPBES.R::table_dt(caption = "dois_not_in_oa")

Of these -628 are not valid. These are:

Show the code

data.frame(
    Type = "doi",
    Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', metrics$dois_not_in_oa[!(metrics$dois_not_in_oa %in% metrics$dois_valid)], metrics$dois_not_in_oa[!(metrics$dois_not_in_oa %in% metrics$dois_valid)])
) |>
    knitr::kable(
        caption = "Non Valid DOIs in the Bibliography",
        escape = FALSE
    )

Non Valid DOIs in the Bibliography
Type	Identifier
doi	(null)
doi	papers3://publication/doi/10.1890/0012-9658(2006)87%255B1877:MBDICL%255D2.0.CO;2
doi	10.1890/1540-9295(2006)4[402:NOIESU]2.0.CO;2
doi	papers3://publication/uuid/CA7EB3A8-6653-4D9F-8D67-078B72D0E44C
doi	papers3://publication/uuid/E08D15D3-9400-46CC-9415-53917EFD2AAD
doi	27
doi	10.1641/0006-3568(2002)052[0499:pfbcpc]2.0.co;2
doi	papers3://publication/doi/10.1890/07-1861.1
doi	10.1890/1540-9295(2003)001[0322:WGSNE]2.0.CO;2
doi	papers3://publication/uuid/446FBDE9-A213-455C-9E19-D9E5CE196252
doi	10.1093/icesjms/fsr165 Is
doi	10.1890/1540-9295(2007)5[261:LESAWR]2.0.CO;2
doi	ISBN 978-2-940443-37-6
doi	papers3://publication/doi/10.1111/j.1472-4642.2010.00652.x/pdf
doi	papers3://publication/uuid/6F951141-1DA7-4D8C-88D5-8CA47168678B
doi	10.1890/0012-9658(2003)084[1382:HBMFPT]2.0.CO;2
doi	papers3://publication/uuid/BA89106B-3993-4E06-887B-58D768043F7D
doi	papers3://publication/uuid/B10C8691-A371-4683-9171-59942A44CECD
doi	papers3://publication/uuid/34CD9F5D-203B-4B83-AE9E-0199C4922D04
doi	papers3://publication/uuid/D932EDF9-1449-4A9C-A684-16D7FD052C11
doi	10.1577/1548-8446(2004)29[23:fsvpoa]2.0.co;2
doi	papers3://publication/doi/10.1111/j.1365-2664.2010.01936.x
doi	10.1890/1051-0761(2000)010[0689:BICEGC]2.0.CO;2
doi	papers3://publication/uuid/B38AB62C-1E75-4F78-B4AE-A517F0F7D438
doi	papers3://publication/uuid/27A75C51-DD7A-46A7-8A7F-7663C2A7FFD3
doi	10.1641/0006-3568(2001)051[0933:teotwa]2.0.co;2

TODO Finally we check, if these dois exist but are not ingested into OpanAlex. This is done using the doi.org resolver This is disabled at the moment.

Show the code

to_check <- bibliography$dois[!(bibliography$dois %in% dois_works)]

dois_valid <- IPBES.R::doi_valid(bibliography$dois)
dois_openalex <- bibliography$dois %in% dois_works
names(dois_openalex) <- bibliography$dois

dois_exist <- IPBES.R::doi_exists(to_check, cache_file = file.path(".", "cache", "doi_exist.rds"))
dois_not_retracted <- IPBES.R::doi_not_retracted(bibliography$dois, cache_file = file.path(".", "cache", "doi_not_retracted.rds"))

sprintf(
    fmt = paste(
        "Number of references: \t\t %d",
        "Number of DOIs: \t\t %d",
        "Number of Duplicate DOIs: \t %d",
        "Number of DOIs in OpenAlex: \t %d ( %f %)",
        "Number of Existing DOIs: \t %d",
        "Number of Retracted DOIs: \t %d",
        "Percentage of Duplicate DOIs: \t %f",
        sep = "\n"
    ),
    nrow(bibliography),
    sum(!is.na(bibliography$dois)),
    length(bibliography$dois) - length(unique((bibliography$dois))),
    sum(dois_openalex), 100 * sum(dois_openalex) / nrow(bibliography),
    sum(dois_exist),
    sum(!dois_not_retracted),
    ((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100
) |> cat()

Show the code

oldopts <- options(knitr.kable.NA = "")
data.frame(
    metrics = c(
        "# References",
        "**DOI**",
        "# DOIs",
        "# Duplicate DOIs",
        "# Existing DOIs",
        "# Retracted DOIs",
        "% Duplicate DOIs",
        "**ISBN**",
        "# ISBNs",
        "# Duplicate ISBNs",
        "**ISSN**",
        "# ISSNs",
        "# Duplicate ISSNs"
    ),
    Value = c(
        nrow(bibliography),
        NA,
        sum(!is.na(bibliography$dois)),
        length(bibliography$dois) - length(unique((bibliography$dois))),
        sum(dois_exist),
        sum(!dois_not_retracted),
        ((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100,
        NA,
        sum(!is.na(bibliography$isbns)),
        length(bibliography$isbns) - length(unique((bibliography$isbns))),
        NA,
        sum(!is.na(bibliography$issns)),
        length(bibliography$issns) - length(unique((bibliography$issns)))
    )
) |>
    knitr::kable(
        caption = "Cleanliness of the Bibliography",
    )
options(oldopts)

Contentual and Bibliographic analysis

Publication types

Show the code

bibliography$bibliography |>
    dplyr::group_by(
        Item.Type
    ) |>
    dplyr::summarize(
        count = n()
    ) |>
    dplyr::arrange(
        desc(count)
    ) |>
    knitr::kable()

Item.Type	count
journalArticle	851
book	129
report	87
bookSection	29
conferencePaper	3
thesis	1

Year of Publication

Show the code

params$figure_pub_year

NULL

Access Status of References

This is checked by using the OpenAlex retrieved works. Therefore it is li=mited to the works that are on OpenAlex. At the moment, only references with a DOI were retrieved from OpenAlex.

Show the code

params$figure_oa_status

NULL

50 Most often cited Journals

Show the code

params$figure_top_journals

NULL

This table contains all Journals as specified in the Zotero database.

Show the code

params$figure_top_journals_data |>
    IPBES.R::table_dt("cited_journals")

TODO Coutries of Institutes of all authors

This plot only contains the countries with more than 10 references.

Show the code

#|
#| fig-height: 10
#| fig-width: 10

params$figure_top_countries

This table contains all countries and the number of authorship.

Show the code

params$figure_top_country_data |>
    IPBES.R::table_dt("top_countries")